User guide

Running F2D requires the selection of a seed (initial fragment) and atoms to start growing.
To select the seed, you have to first select the target 3D structure (crystal from the protein to inhibit).

Parameter selection

  • 1

    Target selection

    Enter a protein gene name (e.g. ABL1) to display all associated PDB.

  • 2

    PDB selection

    Select a PDB ID to display all seeds (i.e. hinge bound fragments).

  • 3

    Seed selection

    Choose a seed to display starting atoms (i.e. atoms with potential bonds with other fragments).

  • 4

    Atom selection

    Select starting atoms, then, all parameters are set to run F2D.

Results

  • 1

    Summary table

    This table summarizes parameters chosen to run Frags2Drugs, the date when the calculation has been done and the number of molecules generated. SDF file containing all generated molecules can be downloaded.

  • 2

    Generated molecules

    Molecules generated by Frags2Drugs and violating no more than 2 PKIDB guidelines are displayed.

  • 3

    Molecule details

    Details are molecule in 2D and 3D representations, its descriptors and comparison with PKIDB guidelines. Molecule detailed can downloaded in SDF format. All fragments combined to create this molecule are displayed, and the starting seed is colored in blue.